msPurity
This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see msPurity.
Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics
Bioconductor version: 3.14
msPurity R package was developed to: 1) Assess the spectral quality of fragmentation spectra by evaluating the "precursor ion purity". 2) Process fragmentation spectra. 3) Perform spectral matching. What is precursor ion purity? -What we call "Precursor ion purity" is a measure of the contribution of a selected precursor peak in an isolation window used for fragmentation. The simple calculation involves dividing the intensity of the selected precursor peak by the total intensity of the isolation window. When assessing MS/MS spectra this calculation is done before and after the MS/MS scan of interest and the purity is interpolated at the recorded time of the MS/MS acquisition. Additionally, isotopic peaks can be removed, low abundance peaks are removed that are thought to have limited contribution to the resulting MS/MS spectra and the isolation efficiency of the mass spectrometer can be used to normalise the intensities used for the calculation.
Author: Thomas N. Lawson [aut, cre] 
, Ralf Weber [ctb], Martin Jones [ctb], Julien Saint-Vanne [ctb], Andris Jankevics [ctb], Mark Viant [ths], Warwick Dunn [ths]
Maintainer: Thomas N. Lawson <thomas.nigel.lawson at gmail.com>
citation("msPurity")):
Installation
To install this package, start R (version "4.1") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("msPurity")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("msPurity")| msPurity | HTML | R Script |
| msPurity spectral database schema | HTML | R Script |
| msPurity spectral matching | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | MassSpectrometry, Metabolomics, Software |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (7.5 years) |
| License | GPL-3 + file LICENSE |
| Depends | Rcpp |
| Imports | plyr, dplyr, dbplyr, magrittr, foreach, parallel, doSNOW, stringr, mzR, reshape2, fastcluster, ggplot2, DBI, RSQLite, uuid, jsonlite |
| System Requirements | |
| URL | https://github.com/computational-metabolomics/msPurity/ |
| Bug Reports | https://github.com/computational-metabolomics/msPurity/issues/new |
See More
| Suggests | MSnbase, testthat, xcms, BiocStyle, knitr, rmarkdown, msPurityData, CAMERA, RPostgres, RMySQL |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | msPurity_1.20.0.tar.gz |
| Windows Binary | msPurity_1.20.0.zip (32- & 64-bit) |
| macOS 10.13 (High Sierra) | msPurity_1.20.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/msPurity |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/msPurity |
| Bioc Package Browser | https://code.bioconductor.org/browse/msPurity/ |
| Package Short Url | https://bioconductor.org/packages/msPurity/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.14 | Source Archive |